runReverseDecon,NanoStringGeoMxSet-method {SpatialDecon} | R Documentation

## Run reversedecon on a NanostringGeomxSet object

### Description

A wrapper for applying reversedecon to a NanostringGeomxSet object.

### Usage

    ## S4 method for signature 'NanoStringGeoMxSet'
    runReverseDecon(object, norm_elt = NULL, beta, epsilon = NULL)

### Arguments

`object` | A NanostringGeomxSet object.
`norm_elt` | normalized data element in assayData.
`beta` | Matrix of cell abundance estimates, with cells in columns and observations in rows. Columns are aligned to "norm".
`epsilon` | All y and yhat values are thresholded up to this point when performing decon. Essentially says, "ignore variability in counts below this threshold."

### Value

a valid GeoMx S4 object including the following items:

- in fData

  - coefs, a matrix of coefficients for genes * cells, where element i,j is interpreted as "every unit increase in cell score j is expected to increase expression of gene i by _".

  - cors, a vector giving each gene's correlation between fitted and observed expression

  - resid.sd, a vector of each gene's residual SD, a metric of how much variability genes have independend of cell mixing.

- in assayData

  - yhat, a matrix of fitted values, in the same dimension as norm

  - resids, a matrix of log2-scale residuals from the reverse decon fit, in the same dimension as norm

### Examples

    library(GeomxTools)
    datadir <- system.file("extdata", "DSP_NGS_Example_Data", package = "GeomxTools")
    demoData <- readRDS(file.path(datadir, "/demoData.rds"))

    demoData <- shiftCountsOne(demoData)
    target_demoData <- aggregateCounts(demoData)

    target_demoData <- normalize(target_demoData, "quant")

    # run basic decon:
    res0 <- runspatialdecon(object = target_demoData,
                            norm_elt = "exprs_norm",
                            raw_elt = "exprs")

    # run reverse decon:
    target_demoData <- runReverseDecon(object = target_demoData,
                                       norm_elt = "exprs_norm",
                                       beta = pData(res0)$beta)

[Package SpatialDecon version 1.4.3 Index]